User: doctor.dee005

gravatar for doctor.dee005
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Location:
Bioinformatics Center, Pune
Last seen:
2 days, 6 hours ago
Joined:
1 year, 9 months ago
Email:
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Posts by doctor.dee005

<prev • 11 results • page 1 of 2 • next >
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gene copy numbers in an genome
... Where can I find gene copy numbers of each gene found in the genome? If any way to extract information from reliable databases? ...
genome gene next-gen written 8 days ago by doctor.dee00520
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BPGA - how to update KEGG and COG database?
... I am using BPGA tool for pan genome analysis. It uses COG and KEGG database to find significant functional genes in genomes. The tool provide its own KEGG and COG files. I want to take updated versions. Is there any way to do that? **If I could get KEGG protein sequences with KO'S then also it wou ...
bpga assembly microbes sequencing written 21 days ago by doctor.dee00520
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download KEGG genes sequence in fasta format
... Is there any tool or script or package to download the KEGG gene sequence in fasta format by KO ids? I have list of KO's. ...
genome gene sequence kegg written 21 days ago by doctor.dee00520
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Answer: A: BPGA - Bacterial Pan Genome Analysis pipeline
... How can I update COG and KEGG data for using it with BPGA? ...
written 22 days ago by doctor.dee00520
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Answer: A: Extract V3-V4 regions from 16s sequences
... You can find the script [here][1]. Just install emboss toolkit or make sure you have fuzznuc in your path. Let me know your experience, I will improve it if needed. This script uses given primer sets (reverse and forward) to extract the region which can be amplified. So you can use the primers accor ...
written 5 weeks ago by doctor.dee00520
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Genome annotation to KEGG KO ids
... I have a complete genome sequence of an organism well annotated. I want to get KO ids for eanch ezymes found in the genome. And what if I have partially annotated sequence? Any ideas are welcomed. ...
genome assembly sequence kegg pathway written 6 weeks ago by doctor.dee00520 • updated 6 weeks ago by lieven.sterck1.7k
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Comment: A: Extract V3-V4 regions from 16s sequences
... I had downloaded greengenes, SILVA and RDP full length 16S rRNA gene databases and used universal primers of V4 regions to scan against each sequence by fuzznuc (emboss toolkit). If required I can share my python script. ...
written 6 weeks ago by doctor.dee00520
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Comment: C: How to use stringdb offline for finding interactions between 4000 protein sequen
... I have downloaded interactions. Now I have sequences of about 4-5K proteins. I want to scan all those sequences and predict a PPI. As the webservice of stringDB does not support such large size of input, I have to do it offline. Just simply my question is ------------ How to use PPI data to scan ag ...
written 10 months ago by doctor.dee00520
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How to use stringdb offline for finding interactions between 4000 protein sequences?
... Web server limits the search for more sequences. I am new to this database. I wanted to predict protein-protein interactions between around 4000 protein sequences which are predicted by GenMark. ...
sequence written 10 months ago by doctor.dee00520 • updated 10 months ago by genomax49k
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Non Epitope databases
... Which are databases or sources for experimentally determined t cell non epitopes peptides? ...
epitope prediction written 16 months ago by doctor.dee00520

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